Synechocystis PCC 6083 (Synechocystis) cells produce hydrogen in the absence of light, during oxygen deprivation. The enzyme responsible for the hydrogen production in this strain is the hox hydrogenase, which catalyses the simple H2↔2H++2e− redox reaction. This bidirectional hydrogenase is also found in Synechococcus elongatus PCC 7942 (Synechococcus) and Acaryochloris marina (Acaryochloris). However, we could not detect in vivo hydrogen production neither in Synechococcus nor in Acaryochloris. In Synechocystis, in a dark, hypoxic environment a strongly reduced plastoquinon (PQ) pool implies that there are excess electrons and protons available for the hydrogenase, which is present in the cell in an elevated level shown by RT-PCR. Conversely, we found that the hox genes are suppressed in Synechococcus under the same conditions. In Acaryochloris a dark hypoxic environment induces the hox genes. Despite the elevated enzyme level in Acaryochloris H2 production is undetectable, likely because of the shortage of reducing equivalents available for the hydrogenase that is indicated by a feeble PQ pool reduction.